The Encryption branch under Configuration - File Handling has the following options:
Delete original file(s) after encrypting
This setting determines if the original plain-text file should be deleted automatically after it is successfully encrypted.
Delete backup file(s) after encrypting
This setting determines if backups of the original plain-text file should be deleted automatically after it is successfully encrypted.
Replace encrypted/decrypted file if it exists
If this option is selected, any files that already exist in the specified path with names and extensions matching the files selected for encryption/decryption would automatically be overwritten.
Automatically re-encrypt file on close
If this option is selected, files that are decrypted prior to editing will automatically be re-encrypted when saved and closed. This option will respect other encryption options set in Configuration as well which pertain to deletion/overwriting of files after encryption.